Archive by Author | Rob

Phenology at scale

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We have launched a number of recent phenology expeditions, as experiments and under our “Labs” section of Notes from Nature. We have gathered some great data from those efforts, and we are now excited to expanded further here, related to two ongoing on research projects. Our first attempt at expansion is now posted as a new expedition entitled, “Predicting Past and Present Phenology I”. So let’s talk about how your help can move forward some great science and informatics endeavors.

The first project is related to work to integrate phenological information coming from multiple sources. Over the past few years, we have been working on building data integration tools in order to bring together data from two different and major observation networks, the National Phenology Network (npn.org) here in the United States, and the Pan-European Phenology Network (http://www.pep725.eu/). Integrating these data is longer, neat story that involved building an ontology for plant phenology (https://www.frontiersin.org/articles/10.3389/fpls.2018.00517/full) and using a set of cool tools to end up with a new portal to find integrated phenology data (plantphenology.org). We are excited to now integrate herbarium data with the observation records as a next step. That will require some extra effort, since herbarium sheets only show parts of plants, not the whole plant, but we are working on the logic of how to do this. And we want to showcase citizen science efforts to help build these coordinated data resources, which is where you come in. We’ll be integrating the results of your efforts right into plantphenology.org!

But wait, there is more…

We are also working on a project looking at how regional urbanization along with climate change can both impact phenology. Urbanization can impact phenological timing of plants via especially increasing temperatures through the urban heat island effect. How such urbanization and overall climate changes impact phenology can be examined in the present looking at spatial patterns, but its very exciting to also be able to look at these questions temporally as well. How have trends over time in urbanization impacted phenology trends e.g. earlier flowering. Herbarium specimens can provide that critical look at the trends across time. We have explicitly chosen groups with relatively rich records in the 19th and 20th centuries that are also well studied today. We will presenting some of the results of this work over upcoming blog posts.

A couple notes about this expedition and the ones to follow. First, we are still experimenting with how to best capture phenology information from specimens, and feedback on how easy or hard you find the expedition(s) is much appreciated. Second, we have decided to present more than one taxa in the same expedition. We know this makes it challenging, and if you have issues, please let us know. We haven’t provided extensive help per species, but have tried to point you to some possible sources to check out more information.

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Nitrogen Fixers Part 3 — Missouri Botanic Garden Goodness

 Our next expedition featuring plants from the Nitrogen Fixing clade is here!  As you know, we have been busily collecting samples from herbarium specimens that will be used to look at the genomes of these plants.  We are looking in particular for the genes that are responsible for creating the root nodules that house nitrogen-fixing bacteria.  This symbiosis has allowed plants with these nitrogen fixing bacteria to survive in places where they usually cannot.

We plan to look at a portion of the genome for more than ten thousand species of the 35,000 or so in the nitrogen fixing group (which forms a natural grouping).  The photo below shows two of our champion samplers during our best day collecting ever – 322 species were sampled.  When we sample, we have to look through folders of herbarium sheets to find specimens that are relatively recent and that are in good shape for taking a small piece of tissue.  The specimen photos you are helping to digitize all have QR code coin envelopes in them, as you have noticed, and those are the same envelopes (with a little bit of tissue tucked inside) as in the photo.
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This new expedition (the third Nitrogen Fixing expedition) features specimens from the Missouri Botanic Gardens (MOBOT), which houses a fabulous collection of plants from around the world.  MOBOT has databased a lot of their material, and for us to be able to access databased specimens, we need to be able to reference the last name of the collector of the specimen and the collector number.   This makes for a fast expedition since those are the only two pieces of information we need right now.  We also hope you like learning about this remarkable group of plants, and we appreciate the help unraveling one of the most successful symbioses on the planet.

Swipe for Science!

 

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Can you spare a few moments to help identify flowers on images of museum specimens? We need help with a simple task, which will assist researchers who are studying phenology (cycles of events in the natural world).  All you need to do is download the Zooniverse mobile app, load up our first ever fully mobile expeditions, and swipe right if you see flowers and left if you do not.   It may be simple, but it will be a huge help for science.

The species we’ll be focusing on is called evening primrose.  The flowers of the evening primrose open quickly every evening, earning this plant its name.  Its flowering phenology is broadly late Spring through Fall but we don’t yet know much how that varies across geography and during different years with different weather patterns.

Here are more details to help you get started:

  • Download the Zooniverse app from Google Play or the App Store. Picture1
  • Select Nature and scroll to Notes from Nature. You don’t need to create an account if you don’t want to.
  • Select “Phenology II: Evening-primroses”
  • Read through the short tutorial. Be sure to check out the directions by clicking the “?” next to the question.
  • After that you will see an image of a plant specimen. Can you see flowers?  If yes, swipe right, and if no, swipe left.
  • You may need to zoom in to check for flowers. You can tap the image to engage the zoom feature and then use normal gestures to zoom in or out.

We know some folks have helped with this project using our web application, and that is still up and running as well.

Thanks for your time! If you enjoyed this project, then please check out notesfromnature.org.

We <3 New York Botanic Gardens (NYBG) and the first NitFix expedition finished

Back in October, we started an adventure that I am not sure has ever been tried before. We aimed to sample 15,000 species (!) of nitrogen fixing plants, with the goal of assembling one of the largest set of resources to better understand the underlying genomic innovations that led to nitrogen-fixing plants. The main resource we are using are small tissue samples (e.g. leaf and floral material) taken from already-collected samples stored in herbaria. Our first port of call was the New York Botanic Gardens, and the truly awesome staff there, especially Barbara Theirs and Charlie Zimmerman, but we owe thanks to the whole herbarium for making us feel so welcome.  We ❤ NYBG!

Here we are happily sampling:

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We collected about 1400 samples during our first visit, and we since have also begun to extract DNA from those samples. The great news is that we are having a lot of success with extractions, thanks to the hard work of Heather Rose Kates at the Florida Museum. We will talk more about the next steps in further blog posts, but we are excited about that success. We have also visited a lot more herbaria, including ones at Harvard University, the California Academy of Sciences, the Missouri Botanic Gardens, and the Ohio State University. We also just headed back to the New York Botanic Gardens and will be sampling there for many more weeks. We anticipate hitting our half way mark this week – 7500 samples!   That represents a huge amount of work!

The data we are getting from labels is really important for this work. Photo vouchers and labels link the genes to the specimen, both virtually and in a physical sense too. Label data will be used in a lot of the downstream analyses that come from this work and we are so thrilled that you helping this science happen. Nitrogen fixing is a key novel symbioses that really changed the world, we are hoping to learn how that novelty arose, and herbaria and their specimens may be an essential part of the key to telling that story. Your help is so important so a HUGE thanks for your work on the first NitFix expedition. There is already a second one up and a third one soon to follow.

Talking about Talk

We are excited to see all the effort on Notes From Nature in terms of transcription effort, but one thing we’ve mentioned less is just how active everyone has been on Talk.  But the numbers are insane, in the good way.  Today was a record breaking day (we are currently at 203 talk items as of 5pm), and to just get a sense of activity change, below is the talk items per day chart for the past few months (from June 23-November 1).

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To what do we attribute all the talking, especially the big change in the last few weeks?  We aren’t sure, but whatever it is, its great to see.  We love the talking, and we appreciate all your help and willingness to share thoughts, concerns and expertise on the talk channels.

 

Too many eyes and legs!

We have a new expedition up on SPIDERS just in time for Halloween.  Spiders often get a bad rap. They are seen as scary and creepy, especially around Halloween when people decorate their houses and shrubs with fake webs and giant black widows. But spend a few minutes watching them and you will realize spiders are some of the most fascinating and talented animals in your neighborhood. The most conspicuous spiders are the orb weavers that spin webs of concentric circles, like in Charlotte’s Web – though don’t expect to see any advertisements written in these webs. Many of these spiders eat their webs each day, recycling the materials, and rebuild them for the next night’s catch, which they skillfully wrap in silk to snack on later.

Araneus sp _ SD Zoopicture credit San Diego Zoo

Many spider species do not build webs at all. Jumping spiders and wolf spiders are active, visual predators with two, large, forward-facing eyes, to go with their lateral eyes. They capture their prey by pouncing on them. Jumping spiders in particular are very inquisitive and often will investigate objects you set in front of them. Many are brightly colored and have very elaborate courtship displays in which they wave their front legs and thump their abdomens (try a search for “peacock spiders”).

Phidippus sp_Susan Kennedypicture credit Susan Kennedy

Spiders also are unfairly accused of bites and crawling into people’s mouths at night. It is not clear where these urban myths came from, but there is no evidence that spiders infiltrate us while we slumber. As far as bites, it is extremely rare that someone actually finds the suspected spider on, or anywhere near them after a bite. Unless a spider feels trapped with no recourse, it very rarely bites. Even when left with the choice of fighting back or losing a leg, many will choose to lose a leg and run away on seven.

So why the bad rap? Probably because we walk into their sticky webs and find them lurking in the corners of our buildings. And also because they look so incredibly different from us with too many legs and too many eyes.

Finally, thanks for your help with our newest CalBug expedition, although maybe in this case we should call it SpiderCal or ArachniCal for this one instead?

Peter Oboyski, with slight embellishment by Rob Guralnick

Thanks for your help on the “New World Swallowtail Butterflies from the Field Museum of Natural History II” expedition

Butterfly wings are amazing things, made of two connected membranes, with internal nerves, veins and passages for air inside.  On the outside are pigmented scales that attach to this membrane.  Those pigmented scales give butterflies their vibrant colors that continue to amaze us.  When flying, wings are moved by the rapid muscular contraction and expansion of the thorax, providing lift.  

Scales of a butterfly wing.  Photo from:  https://c1.staticflickr.com/3/2081/5773583820_71b9396a52_b.jpg

The shape of butterfly wings have been sculpted by selective forces, both natural and sexual selection.  How wing shape varies due to biotic and abiotic factors has long fascinated biologists, including my post-doctoral student, Hannah Owens.  She has been working on one of the largest accumulations of butterfly wing morphometrics yet attempted, that includes 1000s of specimens.  One reason we can do this work is because of volunteer help transcribing labels that describe where these specimens were collected. With that information, we can also get information on the environment where those specimens were collected.

  We really appreciate the effort to accelerate research on butterfly wing shape, and we’ll be talking more about her work, especially some key questions she can tackle, in a later blog post.   We have another set of images soon available and more about this neat work she is doing. Thanks for your effort to be part of Hannah and her research project, and for being part of Notes of Nature.   We have some more images coming – what we think might be the last batch – and we hope you’d be willing to help again.

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